We recommend avoiding it since nutritional yeast is in most cases Saccharomyces cerevisiae, the same strain which is tested in ImuPro.
Even though nutritional yeast is deactivated, which means that it can´t multiply anymore, it might not have completely lost its antigenicity. It is probably the same like with yeast used in bread which is also inactive after baking but still has its allergic effect. So you better avoid yeast during elimination phase.
When it is reintroduced in the provocation phase you will quickly notice any adverse reaction.